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<h1 class="title toc-ignore">Using renv with Bioconductor</h1>



<p><code>renv</code> has been designed to work together as seamlessly as
possible with the <a href="https://bioconductor.org/">Bioconductor</a>
project. This vignette outlines some of the extra steps that may be
required when using <code>renv</code> with packages obtained from
Bioconductor.</p>
<div id="initializing-a-project" class="section level2">
<h2>Initializing a Project</h2>
<p>To initialize <code>renv</code> in a project using Bioconductor, you
can pass the <code>bioconductor</code> argument to
<code>renv::init()</code>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># use the latest-available Bioconductor release</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">::</span><span class="fu">init</span>(<span class="at">bioconductor =</span> <span class="cn">TRUE</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"># use a specific version of Bioconductor</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">::</span><span class="fu">init</span>(<span class="at">bioconductor =</span> <span class="st">&quot;3.14&quot;</span>)</span></code></pre></div>
<p>This will tell <code>renv</code> to activate the appropriate
Bioconductor repositories, and to use those repositories when attempting
to restore packages.</p>
</div>
<div id="bioconductor-releases" class="section level2">
<h2>Bioconductor Releases</h2>
<p>Bioconductor prepares different versions of its package repositories,
for use with different versions of R. The version of Bioconductor used
within a particular <code>renv</code> project is stored both as a
project setting, and also within the project lockfile. This allows you
to “lock” a particular project to a particular Bioconductor release,
even as new Bioconductor releases are made available for newer versions
of R.</p>
<p>To set the version of Bioconductor used in a project, you can
use:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">::</span>settings<span class="sc">$</span><span class="fu">bioconductor.version</span>(<span class="st">&quot;3.14&quot;</span>)</span></code></pre></div>
<p>If you later choose to upgrade R, you may need to upgrade the version
of Bioconductor used as well.</p>
<p>If you want to override the Bioconductor repositories used by
<code>renv</code>, you can also explicitly set the following option:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="at">renv.bioconductor.repos =</span> <span class="fu">c</span>(...))</span></code></pre></div>
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